From 0d5f0c1f20be59b721c9d0ca904d3ac3e2d400cb Mon Sep 17 00:00:00 2001
From: alain viari <viari@aquifex.local>
Date: Wed, 11 Nov 2015 18:51:15 +0100
Subject: [PATCH] summary added in comparison

Former-commit-id: 9a267727234dc9026ce3a54f543e62d8f609945a
Former-commit-id: 556a34a214aea8824f34d4a2c117f09527d88146
---
 detectors/cds/tools/compare/README.txt      | 23 ++++++++++++++++++++
 detectors/cds/tools/compare/go_compare.sh   |  2 +-
 detectors/cds/tools/compare/go_summarize.sh | 24 +++++++++++++++++++++
 3 files changed, 48 insertions(+), 1 deletion(-)
 create mode 100644 detectors/cds/tools/compare/README.txt
 create mode 100755 detectors/cds/tools/compare/go_summarize.sh

diff --git a/detectors/cds/tools/compare/README.txt b/detectors/cds/tools/compare/README.txt
new file mode 100644
index 0000000..201767e
--- /dev/null
+++ b/detectors/cds/tools/compare/README.txt
@@ -0,0 +1,23 @@
+#
+# Compare CDS prediction to Reality
+#
+
+go_compare.sh reference predicted
+
+  reference: Gbk/Embl file
+  predicted: Gbk/Embl file
+
+  output on stdout 
+
+#
+# Summarize comparisons
+#
+  
+go_summarize.sh *.cmp
+
+  *.cmp comparison files (output of go_compare.sh)
+  
+  output :
+    compare.txt : space delimited format summary
+    compare.pdf : graphics summary
+    
diff --git a/detectors/cds/tools/compare/go_compare.sh b/detectors/cds/tools/compare/go_compare.sh
index 9af85ec..1305598 100755
--- a/detectors/cds/tools/compare/go_compare.sh
+++ b/detectors/cds/tools/compare/go_compare.sh
@@ -3,7 +3,7 @@
 # compare CDS annotation in reference file to predicted file
 # annotation file are in Genbank/Embl format
 #
-# usage: go_compare reference predicted
+# usage: go_compare.sh reference predicted
 #
 # output on stdout
 #
diff --git a/detectors/cds/tools/compare/go_summarize.sh b/detectors/cds/tools/compare/go_summarize.sh
new file mode 100755
index 0000000..d6f3ce7
--- /dev/null
+++ b/detectors/cds/tools/compare/go_summarize.sh
@@ -0,0 +1,24 @@
+#
+# summarize comparison
+#
+# run after go_compare.sh
+#
+# usage: go_summarize.sh *.cmp
+#
+#
+unsetenv ORG_SOURCED
+
+setenv ORG_HOME `dirname $0`/../../../..
+source $ORG_HOME/scripts/csh_init.sh
+
+NeedArg 1
+
+egrep '^#|^MATCH' $* | awk -f $LIB_DIR/summary.cmp.awk > compare.txt
+
+$LIB_DIR/summarize_cmp.r 
+
+
+
+exit 0
+
+